CC Integration Update

[JoshLoecker]

This pull request introduces several enhancements and refactors to create_context_specific_model.py, focusing on improving flexibility in gene expression handling, boundary reaction validation, and robustness in solver configuration

• Added support for .h5ad gene expression files, allowing direct loading of single-cell data
• Introduced the force_add_base_exchange_reactions option, allowing basal exchange reactions to be forcibly included in the output model
• Improved validation for boundary reaction files: now checks for extra columns, supports legacy column names, and ensures compartment names are recognized, enhancing robustness and backward compatibility
• Updated solver tolerance assignment to only set optimality tolerance for GUROBI, and improved error handling when setting the model objective
• Changed figure output path arguments in distribution combination functions to accept None, and added conditional directory creation, allowing optional figure output and preventing errors when not required (main/como/combine_distributions.py)

Miscellaneous:

• Cleaned up imports and removed unused typing constructs for clarity and maintainability